title: Analysis of Transcriptomics and Rhizosphere Fungal Diversity in Different Tissues of Blueberry under Cadmium Stress

city: JiLin

first: Chen

last: Shaopeng

address: 77 Hanlin Road, Economic and Technological Development Zone, Jilin City, Jilin Province

institute: Jilin Agricultural Science and Technology College

summary: In this study, blueberry transcriptomics and rhizosphere fungal diversity were analyzed by simulated potting method to treat blueberries with Cd stress, and the content of Fe, Mn, Cu, Zn and Cd in each tissue, soil and DGT of blueberries were determined. , Combined with transcriptomics for correlation analysis. A total of 84374 annotated genes were obtained in blueberry roots, stems, leaves and fruits, of which 3370 DEGs were found, and DEGs in the stem accounted for the highest proportion, totaling 2521. The annotation results show that these DEGs are mainly concentrated in a series of metabolic pathways related to signal transduction, defense and pathogenic response. Blueberries transfer excess Cd from the root to the stem for storage. The stem contains the highest Cd content, which is consistent with the transcriptomics analysis results, while the fruit contains the lowest Cd content. Correlation analysis between heavy metal content and transcriptomics results in each tissue was carried out, and a series of genes related to Cd regulation were screened. The blueberry root system relies on mycorrhiza to absorb nutrients in the soil. The intervention of Cd has severely affected the microflora structure of the blueberry rhizosphere soil. Coniochaetaceae, which is extremely tolerant, has gradually become the dominant population.

overall_design: Apply CdSO4 in the form of an aqueous solution to control the Cd2+ concentration in the soil to 400.00mg/kg (calculated by the weight of pure metal). The control group is a potted plant (CK) without CdSO4, and the treatment is repeated three times for each group，Collect blueberry roots, branch, leaves and fruits for transcriptome sequencing

first: Shaopeng

last: Chen

first: QianQian

last: Zhuang

first: XiaoLei

last: Chu

first: ZhiXin

last: Ju

first: Tao

last: Dong


title: Identification of LPA-LPAR-GNA12 driven Gene signatures and Key Pathways in Ovarian Cancer

status: Public on Aug 25 2021

city: Oklahoma City

first: Muralidharan

last: Jayaraman

state: Oklahoma

address: 975 NE 10th Street BRC1401

department: Cell Biology

country: USA

institute: University of Oklahoma Health Sciences Center

summary: Lysophosphatidic acid (LPA) and LPA-receptor (LPAR)-activated G-protein alpha subunits encoded by GNAi2, GNA12, and GNA13 play a crucial role in ovarian cancer progression. While the general signaling mechanism regulated by LPA-LPAR-signaling had previously been characterized, the global transcriptomic network regulated by individual G protein alpha-subunits in ovarian cancer pathophysiology remains largely unknown. To define the specific oncogenic networks regulated by LPA-stimulated GNAi2, GNA12, and GNA13 in ovarian cancer, transcriptomic analyses were carried out using SKOV3 cells in which the expression of GNAi2, GNA12, or GNA134 was silenced in an Agilent SurePrint G3 Human Comparative Genomic Hybridization 8x60 microarray platform.

overall_design: SKOV3 cells were stably knockdown for GNA12, GNA13, GNAi2 and control  was scrabbled DNA. These 4 cell lines were LPA stimulated under normoxia or hypoxia conditions.

first: Danny

last: Dhanasekaran

first: Jihee

last: Ha

first: Mingda

last: Yan


title: Combinations of maternal-specific repressive epigenetic marks in the endosperm control seed dormancy

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

type: Expression profiling by high throughput sequencing

summary: Polycomb Repressive Complex 2 (PRC2)-mediated trimethylation of histone H3 on lysine 27 (H3K27me3) and methylation of histone 3 on lysine 9 (H3K9me) are two repressive epigenetic modifications that are typically localized in distinct regions of the genome. For reasons unknown, however, they co-occur in some organisms and special tissue types. In this study, we show that maternal alleles marked by H3K27me3 in the Arabidopsis endosperm were targeted by the H3K27me3 demethylase REF6 and became activated during germination. In contrast, maternal alleles marked by H3K27me3, H3K9me2, and CHG methylation (CHGm) are likely to be protected from REF6 targeting and remained silenced. Our study unveils that combinations of different repressive epigenetic modifications time a key adaptive trait by modulating access of REF6.

overall_design: Endosperm tissues were dissected from germinating seeds of Arabidopsis thaliana and analysed in two parallel experiments. Firstly, by comparing three replicates of wild type against three replicates of the ref6-1 mutant. Secondly, by comparing three new replicates of wild type against three replicates of the suvh456 mutant. Total RNA was extracted using MagMAX™ Plant RNA Isolation Kit (Thermo Fisher Scientific), and cDNA libraries were constructed using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB). Libraries were sequenced on Illumina NovaSeq platforms as paired-end through Novogene mRNA sequencing services.

first: Sato

last: Hikaru

first: Claudia

last: Köhler


title: The interferon landscape along the respiratory tract impacts the severity of COVID-19

city: Boston

first: Achille

last: Broggi

state: MA

address: 300 Longwood Ave

department: Pediatrics/Immunology

institute: Boston Children's Hospital

summary: Severe COVID-19 is characterized by overproduction of immune mediators, but the role of interferons (IFNs) of the type I (IFN-I) or type III (IFN-III) families remains debated. We scrutinized the production of IFNs along the respiratory tract of COVID-19 patients and found that high levels of IFN-III, and to a lesser extent IFN-I, characterize the upper airways of patients with high viral burden but reduced disease risk or severity. Production of specific IFN-III, but not IFN-I, members denotes patients with a mild pathology and efficiently drives the transcription of genes that protect against SARS-CoV-2. In contrast, compared to subjects with other infectious or non-infectious lung pathologies, IFNs are over-represented in the lower airways of patients with severe COVID-19 that exhibit gene pathways associated with increased apoptosis and decreased proliferation. Our data demonstrate a dynamic production of IFNs in SARS-CoV-2-infected patients, and show IFNs play opposing roles at distinct anatomical sites.

overall_design: For targeted transcriptome sequencing, RNA (15ng) isolated from nasopharingeal swabs and bronchio alveolar lavage fluid (as desceibed below) was retro-transcribed to cDNA using SuperScript VILO cDNA Synthesis Kit (11754-05, Thermo Fisher). Barcoded libraries were prepared using the Ion AmpliSeq Transcriptome Human Gene Expression Kit (A26325, Thermo Fisher) as per the manufacturer’s protocol and sequenced using an Ion S5 system (A27212, Thermo Fisher). Differential gene expression analysis was performed using the Transcriptome Analysis Console (TAC) software with the ampliSeqRNA plugin (ThermoFisher Scientific).

first: Benedetta

last: Sposito

first: Laura

last: Pandolfi

first: Stefania

last: Crotta

first: Nicola

last: Clementi

first: Roberto

last: Ferrarese

first: Sofia

last: Sisti

first: Elena

last: Criscuolo

last: Spreafico

first: Jaclyn

middle: M

last: Long

first: Enju

last: Liu

first: Vanessa

last: Frangipane

last: Saracino

first: Alessandro

last: Ambrosi

first: Sara

last: Bozzini

last: Marongiu

first: Fabio

middle: A

last: Facchini

first: Tommaso

last: Fossali

first: Riccardo

last: Colombo

first: Massimo

first: Janet

last: Chou

last: Tagliabue

first: Antonio

middle: E

last: Pontiroli

first: Andrea

last: Bottazzi

first: Federica

last: Meloni

first: Andreas

last: Wack

first: Nicasio

last: Mancini

first: Ivan

last: Zanoni


title: Experimental Babesia rossi infection induces hemolytic, metabolic, and viral response pathways in the canine host

city: Bethesda

first: Philip

last: Murphy

state: MD

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

summary: Babesia rossi is a leading cause of morbidity and mortality among the canine population of sub-Saharan Africa, but pathogenesis remains poorly understood. Previous studies of B. rossi infection were derived from clinical cases, in which neither the onset of infection nor the infectious inoculum were known. Here, we performed controlled B. rossi inoculations in canines and evaluated disease progression through clinical tests and whole blood transcriptomic profiling. Three subjects were administered a low inoculum (104 parasites) while two received a high (109 parasites). Subjects were monitored for 8 consecutive days; anti-parasite treatment diminazene aceturate was administered on day 4. Blood was drawn prior to inoculation as well as every experimental day for assessment of clinical parameters and transcriptomic profiles. The model recapitulated natural disease manifestations, including pro-inflammatory cytokine storm and metabolic acidosis. Rate of onset and severity were proportional to inoculum. To analyze the temporal dynamics of the transcriptomic host response, we sequenced mRNA extracted from whole blood drawn on days 0, 1, 3, 4, 6, and 8. Differential gene expression, hierarchical clustering, and pathway enrichment analyses identified genes and pathways involved in response to hemolysis, metabolic changes, and several arms of the immune response including innate immunity, adaptive immunity, and response to viral infection. These findings enhance our understanding of B. rossi pathogenesis, identify novel pathways for interventions to reduce disease severity, and establish a new mammalian model of hemolytic inflammatory disease.

overall_design: Blood RNAseq from 5 dog inoculated with Babesia rossi. 3 dogs received low dose, 2 received high dose, dogs wer monitored for 8 days, and RNAseq was performed on days 0 (onset),, 1, 3, 4, 6, and 8.

first: Rachel

middle: L

last: Smith

first: Amelia

last: Goddard

first: Arun

last: Boddapati

first: Steven

last: Brooks

first: Johan

last: Schoeman

first: Justin

last: Lack

first: Andrew

last: Leisewitz

first: Hans

last: Ackerman


title: Downregulation of CRX, a Group 3 specific oncogenic transcription factor, inhibits TGF-b/activin signaling in medulloblastoma cells

status: Public on Aug 26 2021

city: Navi Mumbai

first: Neelam

middle: V

last: Shirsat

state: Maharashtra

address: Kharghar, Sector 21

department: Shirsat Lab

country: India

institute: Advanced Centre for Treatment, Research and Education in Cancer. Tata Memorial Centre

summary: Retina-specific gene expression is the distinguishing characteristic of Group 3 medulloblastoma. CRX, a homeobox transcription factor, is overexpressed specifically in Group 3 tumors. ShRNA-mediated CRX knockdown decreased the expression of seveal retina-specific genes and Group 3 specific genes. CRX knockdown inhibited the TGF-beta/activin signaling pathway, which is known to play oncogenic role in a subset of Group 3 medulloblastoma

overall_design: Expression of CRX was knocked down in D425 and HD-MB03, Group 3 medulloblastoma cell lines using two independent shRNAs using the Tet-pLKO-puro lentiviral vector.  Stable polyclonal populations expressing the shRNA were obtained by transducing the cell lines with the lentiviral particles. Total RNA was prepared from the vector control cells expressing the empty vector and those expressing the shRNA targeting CRX.  Libraries were prepared from the polyA-enriched RNA fraction using the Illumina Truseq RNA library preparation kit and sequenced on the Illumina Hiseq platform

first: Shalaka

last: Masurkar


title: Transcriptome analysis of Indian mulberry leaf tissue

city: BENGALURU

first: KARABA

middle: N

last: NATARAJA

state: KARNATAKA

address: BELLARY ROAD

department: CROP PHYSIOLOGY

institute: UNIVERSITY OF AGRICULTURAL SCIENCES BENGALURU

summary: The mian goal of the study was to identify drought responsive genes of Indian mulberry (Morus alba L.) leaf tissue. Drought stress was imposed at whole plant leve; usig gravimetric approach. Leaf tissue was harvested 14 days post drought stress imposition and used for transcriptome analaysis. Two levels of drought stress (100% and 40% soil field capacity) was maintained by controlled irrigation. The leaf tissue was collected, total RNA was isolated converted to cDNA and used for analysis

overall_design: 4 samples representing 2 treatments (fully irrigated and drought stress ie 100% and 40% field capacity) with two biological replicates each.

first: K

middle: H

last: Dhanyalakshmi

first: H

last: Chaithra

last: Nataraja


title: Cerebral cortex and blood transcriptome changes in mouse neonates prenatally exposed to air pollution particulate matter

city: San Diego

first: Amin

last: Haghani

state: CA

address: 5510 Morehouse Dr

institute: Altos labs

summary:
Background: Prenatal exposure to air pollutants is associated with increased risk for neurodevelopmental and neurodegenerative disorders. However, few studies have identified transcriptional changes related to air pollutant exposure.

Methods: RNA sequencing was used to examine transcriptomic changes in blood and cerebral cortex of three male and three female mouse neonates prenatally exposed to traffic-related nano-sized particulate matter (nPM) compared to three male and three female mouse neonates prenatally exposed to control filter air.

Results: We identified 19 nPM-associated differentially expressed genes (nPM-DEGs) in blood and 124 nPM-DEGs in cerebral cortex. The cerebral cortex transcriptional responses to nPM suggested neuroinflammation involvement, including CREB1, BDNF, and IFN γ genes. Both blood and brain tissues showed nPM transcriptional changes related to DNA damage, oxidative stress, and immune responses. Three blood nPM-DEGs showed a canonical correlation of 0.98 with 14 nPM-DEGS in the cerebral cortex, suggesting a convergence of gene expression changes in blood and cerebral cortex. Exploratory sex-stratified analyses suggested a higher number of nPM-DEGs in female cerebral cortex than male cerebral cortex. The sex-stratified analyses identified 2 nPM-DEGs (Rgl2 and Gm37534) shared between blood and cerebral cortex in a sex-dependent manner.

Conclusions: Our findings suggest that prenatal nPM exposure induces transcriptional changes in the cerebral cortex, some of which are also observed in blood. Further research is needed to replicate nPM-induced transcriptional changes with additional biologically relevant time points for brain development.

overall_design: Pregrant dams were exposed to nPM during gestational period. The effects were studied in neonate pups.

first: Jason

middle: I

last: Feinberg

first: Kristy

last: Lewis

first: Christine

last: Ladd-Acosta

first: Richard

middle: G

last: Johnson

last: Jaffe

first: Constantinos

last: Sioutas

first: Caleb

last: Finch

first: Daniel

middle: B

last: Campbell

first: Todd

last: Morgan

first: Heather

last: Volk


title: Gene expression in the F1 and F2 mouse hippocampus with intrauterine hyperglycemia exposure

city: Shanghai

first: Kexin

last: Zou

address: 131 Dongan Rd.

department: School of Medicine

country: China

institute: Fudan University

summary: Studies on human and animals suggest associations between gestational diabetes mellitus (GDM) with impaired cognitive performance in offspring. Using a mouse model of diabetes during pregnancy, we found that intrauterine hyperglycemia exposure resulted in memory impairment in both the first filial (F1) males and the second filial (F2) males from the F1 male offspring. The effects of intrauterine hyperglycemia exposure on F1 and F2 hippocampus gene expression were also examined.

overall_design: Hippocampus, male,  16 weeks old.   Three groups,  F1 offsprings of GDM (F1-GDM) ，F2 offsprings of GDM (F2-GDM) and Control, with 5 replicates per group.

first: Guolian

last: Ding


title: RNA-seq of the overexpressors of site-directed mutant of PhADT

city: Madison

first: Stuti

last: Shrivastava

state: WI

address: 430 Lincoln Drive

department: Botany

institute: University of Wisconsin, Madison

summary: The transcriptional response of the overexpressor of synthetic PhADT, generated through the site-directed mutagenesis of native PhADT(R353A) was compared with wild-type PhADT expressed in the Petunia flowers.

overall_design: Three different genotypes of Petunia flowers, of which two were overexpressors of PhADT, were seqeuenced using Illumina HiSeq platform.

first: Heejin

last: Yoo

first: Natalia

last: Dudareva

first: Amy

last: Marshall-Colón


title: NAD+ supplementation normalizes neuroinflammation and senescence via the cGAS-STING pathway

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Alzheimer's disease (AD) is a severe neurodegenerative disorder. Clinical trials to identify agents to treat AD have failed, and its underlying molecular pathology and etiology remain elusive. Neuroinflammation is thought to play a key role in the progression of AD. Emerging evidence has identified lower Nicotinamide adenine dinucleotide (NAD+) levels as a major factor in neurodegeneration, especially in AD. NAD+ is an important metabolite in all human cells, as it is at the convergence of many central processes in cellular and mitochondrial maintenance, including DNA repair and mitophagy (the degradation of damaged mitochondria). Our previous work found that treatment of 3xTgAD mice with an NAD+ precursor, nicotinamide riboside (NR), can improve key AD features including tau phosphorylation and learning deficits in mice. Here we used the APP/PS1 AD mouse model to interrogate the effect of NR on neuroinflammation. Microarray analysis revealed major changes in pathways and genes associated with inflammation and the APP/PS1 mice had lower NAD+ levels than WT mice. Thus, seven months old mice were treated with NR for five months and their NAD+/NADH ratio increased. Brain neuroinflammation decreased as determined by decreased activation of astrocytes and microglia, decreased pro-inflammatory cytokines and chemokines in the brains of the APP/PS1 mice. NR decreased neuroinflammation by lowering the NLRP3 inflammasome and NF-κB pathways. NR also attenuated DNA damage and apoptosis in the AD mouse brains. NR dramatically decreased senescence in the hippocampus and cortex of AD mice, relative to controls. Recent studies suggest that cyclic GMP-AMP synthase (cGAS) and stimulator of interferon genes (STING) activation are associated with DNA damage and senescence. cGAS-STING was activated in AD mice and decreases after NR treatment. Suggesting that NR can diminish neuroinflammation and senescence through the cGAS-STING pathway. NR treatment also greatly improved cognition and synaptic function in the APP/PS1 mice. We propose that the cGAS-STING pathway should be evaluated as a potential novel therapeutic target in AD.

overall_design: Wild-type (WT) and APP/PS1 AD mice (N=5-7 mice per group) were either treated with nicotinamide riboside (NR, 12 mM) or nothing (CTR) in their drinking water from 7 months of age until sacrifice at 12 months of age, at which point hippocampi and cortical tissue was dissected out for RNA extraction and microarray analysis.

first: Yujun

last: Hou

first: Sofie

last: Lautrup

first: Yue

last: Wang

first: Stephanie

last: Cordonnier

first: Yong

last: Wei

first: Beimeng

last: Yang

first: Mark

middle: P

last: Mattson

first: Deborah

last: Croteau

first: Vilhelm

last: Bohr


title: Fibrotic Remodelling of Epicardial Adipose Tissue in Patients with Atrial Fibrillation: Comparative Analyses of Histological Findings and Computed Tomographic Imaging

city: Yufu

first: Ichitaro

last: Abe

state: Oita

address: 1-1 Idaigaoka, Hasama

department: Department of Cardiology and Clinical Examination

country: Japan

institute: Oita University

summary: Aims: We tested the hypothesis that central-marginal dispersion in adipocyte diameter in epicardial adipose tissue (EAT) would represent fibrotic remodelling of EAT, a crucial state to promote atrial myocardial fibrosis to form a substrate of atrial fibrillation (AF). We also investigated whether the central-marginal EAT density ratio by the analyses of computed tomographic (CT) imaging could predict the central-marginal adipocyte diameter ratio in EAT.  Methods and results: Left atrial appendage samples were obtained from 76 consecutive AF patients during cardiovascular surgery. EAT at central area (Central EAT) and that adjacent to atrial myocardium (Marginal EAT) were evaluated. Compared to the Central EAT, the dimeter of adipocytes was smaller, fibrotic remodeling of EAT (EAT fibrosis) was more severe, and the infiltration of CD3-, CD68-, or α-SMA-positive cells were more abundant in the Marginal EAT. EAT fibrosis positively correlated with adipocyte diameter in the Central EAT, while it negatively correlated with that in the Marginal EAT, resulting in the tightly positive correlation between EAT fibrosis and the ratio of central to marginal adipocyte diameter (C/M diameter ratio) (r=0.73, p<0.01). The C/M diameter ratio was greater in patients with persistent AF (PeAF) than in those with paroxysmal AF (PAF) (p<0.01). The CT density in Central EAT and Marginal EAT was measured and their ratio (C/M density ratio) was calculated. The C/M density ratio correlated tightly with the C/M diameter ratio (r=0.69, p<0.01).   Conclusion: Our results suggest that C/M adipocyte diameter ratio was associated with fibrotic remodeling of EAT and progression of AF. Our results also suggest that C/M adipocyte diameter ratio could be accurately predicted by the analyses of CT findings noninvasively.

overall_design: In three cases, microarray analysis of the two distinct clusters of adipocytes obtained from Central EAT and Marginal EAT was carried out. Central EAT compared to Marginal EAT was caluculated.

first: Yumi

last: Ishii

first: Shintaro

last: Kira

first: Takahiro

last: Oniki

first: Hidekazu

last: Kondo

first: Yasushi

last: Teshima

first: Kunio

last: Yufu

first: Tatsuo

last: Shimada

first: Yoshiki

last: Asayama

first: Shinji

last: Miyamoto

first: Naohiko

last: Takahashi


title: MiR-221/222 suppression induced by activation of the cAMP/PKA/CREB1 pathway is required for cAMP-induced bidirectional differentiation of glioma cells [miRNA]

status: Public on Aug 24 2021

first: Minfeng

last: Shu

state: State...

address: No.131 Dongan Road II Xuhui district

summary:
Factors that increase cAMP levels can induce lineage-specific differentiation of glioma cells into astrocyte-like cells. However, the differentiation pattern and underlying mechanisms remain unclear. Here, we find that cAMP/PKA/CREB1-induced miR-221/222 suppression contributes to the neuron-like differentiation of gliomas. cAMP agonists selectively induced neuron- and astrocyte-like but not oligodendrocyte-like differentiation of C6 glioma cells. PKA inhibitors and CREB1 knockout blocked neuron-like differentiation of glioma cells. cAMP inhibited miR-221/222 in a PKA/CREB1 dependent manner. Importantly, both in vitro and in vivo assays demonstrated that transcriptional suppression of miR-221/222 is required for neuronal differentiation of glioma cells. Our findings suggest that increasing cAMP levels can induce bidirectional differentiation of glioma cells. Furthermore, the miR-221/222 cluster acts as an epigenetic brake during glioma differentiation.
Factors that increase cAMP levels can induce lineage-specific differentiation of glioma cells into astrocyte-like cells. However, the differentiation pattern and underlying mechanisms remain unclear. Here, we find that cAMP/PKA/CREB1-induced miR-221/222 suppression contributes to the neuron-like differentiation of gliomas. cAMP agonists selectively induced neuron- and astrocyte-like but not oligodendrocyte-like differentiation of C6 glioma cells. PKA inhibitors and CREB1 knockout blocked neuron-like differentiation of glioma cells. cAMP inhibited miR-221/222 in a PKA/CREB1 dependent manner. Importantly, both in vitro and in vivo assays demonstrated that transcriptional suppression of miR-221/222 is required for neuronal differentiation of glioma cells. Our findings suggest that increasing cAMP levels can induce bidirectional differentiation of glioma cells. Furthermore, the miR-221/222 cluster acts as an epigenetic brake during glioma differentiation.

overall_design: Examination of miRNAs in C6 glioma cells treated with or without forskolin.

first: Qian

last: Liu

first: Ruotong

last: Tian

first: Panpan

last: Yu


title: Transcriptional profiling of mouse pancreatic tumor cells under nutrient and oxygen deprivation condition

city: New York

first: Jinyang

last: Li

state: New York

address: 1230 York Ave

institute: The Rockefeller University

summary: Transcriptional profiling showed that adaptation to nutrient and oxygen deprivation condition is associated with widespread transcriptional reprogramming resulting in the induction of glycolysis and autophagy and repression of the TCA cycle and biosynthesis

overall_design: Mouse pancreatic tumor cells were cultured in nutrient and oxygen deprivaiton medium for 2 days and 14 days and then were collected for RNAseq.

first: Yogev

last: Sela

first: Ben

last: Stanger


title: Transcriptional profiling of pancreatic tumor cells under nutrient and oxygen deprivation condition

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Transcriptional profiling of human pancreatic tumor cells under nutrient and oxygen deprivation condition

overall_design: Human pancreatic tumor cells were cultured in nutrient and oxygen deprivaiton medium for 2 days and 14 days and then were collected for RNAseq.


title: Transcriptional profiling of human pancreatic tumor cells under nutrient and oxygen deprivation condition, with and without CRISPR targeting of BCL2L1 gene

overall_design: Human pancreatic tumor cells transduced with control or CRISPR targeting BCL2L1 were cultured in nutrient and oxygen deprivation medium for 2 days and then were collected for RNAseq.


title: Molecular characteristics of choledochal cysts in children: transcriptome sequencing

city: ChengDu

first: Yong

last: Lv

state: SiChuan

department: Department of pediatric surgery

institute: West China hospital of Sichuan university

summary:
Choledochal cysts (CC) is a common congenital biliary disease in children, yet the underlying molecular bases for the cystic and fusiform clinical subtypes are unknown.
Methods: RNA-seq has been performed on 22 high-quality CC samples, including 12 cystic CC and 10 fusiform CC samples, to search for molecular features. Weighted gene co-expression network analysis (WGCNA) was performed to identify key modules associated with clinical subtypes. Bioinformatics analysis were conducted to elucidate potential mechanisms. Then, we constructed protein–protein interaction (PPI) network to identify candidate hub genes related to CC. Finally, we used the support vector machine (SVM) to eliminate redundant features and screen out the hub genes. The hub gene expression was determined in CC patients through quantitative real-time PCR.
Results: For the first time, we have described the transcriptome characteristics of CC. These results suggest that cystic CC and fusiform CC have different molecular mechanisms. The bi-omics identified novel candidate genes and pathways might be helpful for personalized treatment and are of great clinical significance for CC.

overall_design: RNA sequencing of 12 cystic choledochal cysts and 10 fusiform choledochal cysts samples.

first: Jing

last: Chen

first: Bo

last: Xiang


title: The age of the bone marrow microenvironment influences B-cell acute lymphoblastic leukemia progression via CXCR5-CXCL13 [RNA-Seq]

city: Heidelberg

first: Mark

last: Hartmann

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center (DKFZ)

summary: We performed RNA sequencing to determine the alteration in the molecular landscape in young versus old macrophages.

overall_design: Young versus old BM macrophages were obtained by crushing femora, tibiae, and humeri of mice in phosphate-buffered saline (PBS) using mortar and pestle and then expanded in alpha-MEM medium supplemented with 20% fetal bovine serum, 1% penicillin/streptomycin and 1% L-glutamine, once non-adherent cells were removed. The immunophenotype of the adherent cells was confirmed by the following immunophenotype: F4/80+ CD169+.

first: Joschka

last: Hey

first: Kersten

last: Breuer

first: Costanza

last: Zanetti

first: Christoph

last: Plass

first: Daniela

middle: S

last: Krause

first: Daniel

last: Lipka


title: Ectopic expression of Snord115 in choroid plexus interferes with editing but not splicing of 5-Ht2c receptor pre-mRNA in mice

city: Muenster

first: Timofey

middle: S.

last: Rozhdestvensky

state: NRW

address: Von-Esmarch-Str. 56

department: University of Muenster

institute: Medical Faculty, Core Facility Transgenic animal and genetic engineering Models (TRAM)

summary: Serotonin 5-HT2C receptor is a G-protein coupled excitatory receptor that regulates several biochemical pathways and has been implicated in obesity, mental state, sleep cycles, autism, neuropsychiatric disorders and neurodegenerative diseases. The activity of 5-HT2CR is regulated via alternative splicing and A to I editing of exon Vb of its pre-mRNA. Snord115 is a small nucleolar RNA that is expressed in mouse neurons and displays an 18-nucleotide base complementary to exon Vb of 5-HT2CR pre-mRNA. For almost two decades this putative guide element of Snord115 has wandered like a ghost through the literature in attempts to elucidate the biological significance of this complementarity. In mice, Snord115 is expressed in neurons and absent in the choroid plexus where, in contrast, 5-Ht2cr mRNA is highly abundant. Here we report the analysis of 5-Ht2cr pre-mRNA posttranscriptional processing via RNA deep sequencing in a mouse model that ectopically expresses Snord115 in the choroid plexus. In contrast to previous reports, our analysis demonstrated that Snord115 does not control alternative splicing of 5-Ht2cr pre-mRNA in vivo. We identified a modest, yet statistically significant reduction of 5-Ht2cr pre-mRNA A to I editing at the major A, B, C and D sites. We suggest that Snord115 and exon Vb of 5Ht2cr pre-mRNA form a double-stranded structure that is subject to ADAR-mediated A to I editing. To the best of our knowledge, this is the first comprehensive Snord115 gain-of-function analysis based on in vivo mouse models.

overall_design: Comparison of two mouse models by RNA deep sequencing

first: Carsten

last: Raabe

first: Reinhard

last: Voss

first: Delf-Magnus

last: Kummerfeld

first: Juergen

last: Brosius

first: Chenna

middle: R

last: Galiveti

first: Anna

last: Wolters

first: Jochen

last: Seggewiss

first: Andreas

last: Huge

first: Boris

last: Skryabin


title: Activation of FcRn mediates a primary resistance response to sorafenib in hepatocellular carcinoma by single-cell RNA sequencing

city: Changchun

first: Xin

last: Guan

address: No.1163 Xinmin Street

institute: School of Pharmaceutical Sciences, Jilin University

summary: Sorafenib is the first-line therapeutic option for advanced hepatocellular carcinoma (HCC). Many patients exhibit a primary resistance response after initial treatment. In previous studies, compared to acquired resistance, the mechanism of primary resistance is unclear. The present study aimed to evaluate the response of patient samples to sorafenib by patient-derived xenograft (PDX) models, and the difference between the sorafenib primary resistance group and the sorafenib sensitive group was analyzed at the single-cell level using single-cell sequencing technology. A special cell cluster may be differentiated by the liver bud hepatic cells, and the JUN transcription factors in this cell cluster were highly activated. The ALB is secreted by other cell clusters, and the cluster stimulates FcRn complex receptor to activate the HIF pathway and cell proliferation, resulting in poor response to sorafenib. These findings are validated by both cell communication analysis and experiments. Thus, the current studies provided a novel approach for the treatment of sorafenib-resistant HCC.

overall_design: Comparison of single-cell sequencing between sorafenib primary resistance group and sorafenib sensitive group

first: Yi

last: Wu

first: Sun

last: Fei

first: Chongyang

last: Liang


title: Transcriptomic changes in SJRHB015721_X1 human FN-RMS following DBX1 knock-down

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

summary: DBX1 is a transcriptional repressor whose role in human cancer is poorly understood. DBX1 is highly expressed in FN-RMS. Here, we depleted DBX1 expression with 2 shRNAs targeting DBX1 in a human FN-RMS cell line we derived from a PDX - SJRHB015721_X1. We determined the transcriptional changes using a Clariom S human microarray.

overall_design: One of two shRNAs targeting DBX1 (or a scramble control) were transduced into SJRHB015721_X1 cells. RNA was harvested 72 hours later using Qiagen's miRNeasy RNA isoloation kit.

first: Mark

last: Hatley


title: Quantitative assessment of transcriptomic differences between ASPcKO and ASPcKOP7cKO flow cytometry-sorted murine FN-RMSs by RNA sequencing

summary: We report the transcriptomic differences between ASPcKO and ASPcKOP7cKO flow cytometry-sorted FN-RMSs by RNA sequencing. The goal of this study is to determine what role Pax7 loss has on Pten-deficient, Hedgehog-activated murine FN-RMS tumors. These results provide implications for the transcriptomic program driven by Pax7 in dictating FN-RMS tumor fate.

overall_design: Two different tumor models are described here - both driven by a constitutive, activated Smoothened allele (SmoM2) under the control of aP2-Cre. In one model, there is only the addition of Pten floxed alleles whereas in the other model there is Pten and Pax7 floxed alleles. A tdTomato allele is also bred into these mice to indelibly mark cells that have expressed aP2-Cre, For the experiment, four tumors from both tumor genotypes (ASPcKO and ASPcKOP7cKO) (8 total tumors) were flow cytometry-sorted and collected based on tdTomato+/PECAM1-APC-(negative) sorting to remove any endothelial cell contamination. These sorted tumor cells were then prepped for low input RNA sequencing.

first: Casey

last: Langdon


title: Insulin response in mouse liver

city: Fukuoka

first: Fumiko

last: Matsuzaki

address: 3-1-1 Maidashi, Higashi-ku

institute: Kyushu University

summary: An effective combination of multi-omic datasets can enhance our understanding of complex biological phenomena. To build a context-dependent network with multiple omic layers, i.e., a trans-omic network, we performed phosphoproteomics, transcriptomics, proteomics, and metabolomics of murine liver for 4 h after insulin administration and integrated the time series. Structural characteristics and dynamic nature of the network were analyzed to elucidate the impact of insulin. Early and prominent changes in protein phosphorylation and persistent and asynchronous changes in mRNA and protein levels through non-transcriptional mechanisms indicate enhanced crosstalk between phosphorylation-mediated signaling and protein expression regulation. Metabolic response shows different temporal regulation with transient increases at early time points across categories and enhanced response in the amino acid and nucleotide categories at later time points due to process convergence. This extensive and dynamic view of the trans-omic network elucidates prominent regulatory mechanisms that drive insulin responses through intricate interlayer coordination.

overall_design: RNA-seq of mouse liver over a period of four hours after insulin/PBS administration. For each condition (insulin/PBS), data was collected at five time points with biological triplicates (total of thirty samples).

first: Kazumitsu

last: Maehara

first: Yasuyuki

last: Ohkawa

first: Hiroyuki

last: Kubota


title: Differences in gene expression between ASP WT and ASPcKO tumors

summary: To further examine the consequences of Pten loss in a Hedgehog driven, murine FN-RMS, we used microarrays to determine the transcriptomic differences between our aP2-Cre;SmoM2 FN-RMS model (Hatley et al. 2012, Cancer Cell) and aP2-Cre; SmoM2; Pten flox/flox FN-RMSs.

overall_design: Four ASP wild-type and four ASPcKO tumors were removed, flash frozen in liquid nitrogen and pulverized in a TissueLyzer. RNA was extracted with Qiagen's miRNeasy RNA Elution Kit.


title: The age of the bone marrow microenvironment influences B-cell acute lymphoblastic leukemia progression via CXCR5-CXCL13

last: Hartmann

type: Genome binding/occupancy profiling by high throughput sequencing


title: Synthetic essentiality between PTEN and core dependency factor PAX7 dictates rhabdomyosarcoma identity


title: The age of the bone marrow microenvironment influences B-cell acute lymphoblastic leukemia progression via CXCR5-CXCL13 [ATAC-Seq]

summary: We performed ATAC sequencing to determine if epigenetic changes regulate the function of  young versus old macrophages.

first: Joschka

last: Hey

first: Kersten

last: Breuer

first: Costanza

last: Zanetti

first: Christoph

last: Plass

first: Daniela

last: Krause

first: Daniel

last: Lipka


title: Efferocytosis fuels malignant pleural effusion through TIMP1

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

institute: Universitätsklinikum Hamburg-Eppendorf

summary: Malignant Pleural Effusion (MPE) results from the capacity of several human cancers to metastasize to the pleural cavity. The median survival is 3-12 months and no effective treatments are currently available. Immune-based therapies have failed until now, reflecting our insufficient understanding of the basic immunological mechanisms leading to MPE progression. Here, we show that phagocytosis of apoptotic cells in the pleural cavity fuels the progression of MPE. We found that efferocytosis through the receptor tyrosine kinases AXL and MERTK in macrophages led to the production of IL-10. Using single cell RNA-Seq, we revealed that IL-10 is indeed produced by four distinct pleural cavity macrophage subpopulations characterized by different metabolic states and cell chemotaxis properties. In turn, IL-10 acts on dendritic cells (DCs) inducing the production of tissue inhibitor of metalloproteinases 1 (TIMP1). Genetic ablation of AXL and MERTK in macrophages or IL-10 receptor in DCs or TIMP1 significantly reduced MPE progression. Taken together, our results delineate an inflammatory cascade – from the clearance of apoptotic cells by macrophages, to production of IL-10, to induction of TIMP1 in DCs – that facilitates MPE progression. This inflammatory cascade offers a series of targets for therapies which aim at preventing or treating MPE.

overall_design: We induced malignant pleural effusion in mice by injecting tumor cells into the pleural cavity of anaesthesized mice. After 10 days, we euthanized the mice, aspirated the pleural liquid, extracted myeloid cells and performed single cell sequencing.

first: Lilan

last: Zhao

first: Anastasios

middle: D

last: Giannou

first: Yang

last: Xu

first: Ahmad

last: Shiri

first: Imke

last: Liebold

first: Lidia

last: Bosurgi

first: Samuel

last: Huber

first: Nicola

last: Gagliani


title: MKN7_EB by EHF knockdown

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University


title: Expression data from YTHDF1 or YTHDF2 down-regulated PC9

city: Hamamatsu

first: Kazuo

last: Tsuchiya

department: Tumor pathology

institute: Hamamatsu University School of Medicine

summary:
The human YTH domain family protein (YTHDF) family is RNA binding protein which specifically recognizes N6-methyladenosine (m6A), and exerts distinct roles in eukaryocytes; YTHDF1 promotes the translation of m6A modified mRNAs collaborating with initiation factors, and YTHDF2 reduces the stability of the m6A-modified transcripts.
We used the Nanostring nCounter to detail the differential gene expression by YTHDF1 and YTHDF2.

overall_design: Total RNA were extracted from YTHDF1 or YTHDF2 knockdown PC9 cells at 48 h after transfection.

first: Haruhiko

last: Sugimura


title: Continuous expression of reprogramming factors OSKM induces and maintains mouse pluripotency without specific growth factors and signaling inhibitors

city: BeiJing

first: Mao

last: Yihuan

address: No. 3 A, Datun Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Derivation and maintenance of pluripotent stem cells (PSCs) including embryonic stem cells(ESCs) and (iPSCs) usually requires optimization of complex culture media, which hinders the generation of PSCs from various species. Expression of Oct4, Sox2, Klf4 and c-Myc (OSKM) can reprogram somatic cells into iPSCs, even for species possessing no optimal culture condition. Here we explored whether expression of OSKM could induce and maintain pluripotency without specific growth factors and signaling inhibitors. Tet-On-OSKM/Oct4-GFP Mouse ESCs (mESCs) were derived from the embryos obtained after mating of Tet-On-OSKM mouse and Oct4-GFP mouse under the 2iL ( N2B27 plus MEK inhibitor PD0325901, GSK3β inhibitor ChIR99021, and leukemia inhibitory factor) condition. Tet-On-OSKM mouse was Gt(ROSA)26Sor tm1(rtTA*M2)Jae Col1a1 tm3(tetO-Pou5f1,-Sox2,-Klf4,-Myc)Jae/J(The Jackson Laboratory,011004), and Oct4-GFP mouse was B6;CBA-Tg(Pou5f1-EGFP)2Mnn/J (The Jackson Laboratory,004654).The culture medium of Tet-On-OSKM/Oct4-GFP mouse ESCs was switched from 2iL to N2B27 plus Doxycycline medium (OSKM medium), under which OSKM trangene was activated. These above cells switched from 2iL to OSKM medium were called OSKM-ESCs. Meanwhile 2iL-ESCs (continuely  cultured in 2iL) served as the positive control group. 2iL-ESCs and OSKM-ESCs collected at selective days (d18, 25 and 38) after medium switch were collected for RNA-Seq. Moreover, Tet-On-OSKM mouse embryonic fibroblast (MEF) cells were reprogrammed under OSKM medium (N2B27 plus Doxycycline) and 2iL medium, respectively. The resulting OSKM-iPSCs were reprogrammed and cultured under OSKM medium.The 2iL-iPSCs  were reprogrammed under 2iL plus Doxycycline medium and cultured under 2iL medium (without Doxycycline)once clones were picked up.RNA-Seq of these above samples was conducted to analyze gene expression. We found that via continuous expression of OSKM,OSKM-ESCs and OSKM-iPSCs  propagated stably, expressed pluripotency marker genes, and formed three germ layers in teratomas. Importantly, OSKM-iPSCs could produce gene-modified animals through germline transmission.Transcriptional landscapes of OSKM-iPSCs resembled 2iL-ESCs, and were more similar to those of ESCs cultured in serum/LIF.

overall_design: mRNA profiles of the following samples were collected. Mouse Tet-On-OSKM/Oct4-GFP ESC lines collected at selective days (d18, 25 and 38) after medium switch (2iL-ESCs as positive controls, unchanged; and OSKM-ESCs,  switched from 2iL to N2B27 plus DOX). Tet-On-OSKM MEF cells were reprogrammed. OSKM-iPSCs reprogrammed and cultured under N2B27 plus DOX. 2iL-iPSCs reprogrammed and cultured under 2iL.

first: Yihuan

last: Mao

first: Libin

last: Wang

first: Bei

last: Zhong

first: Ning

last: Yang

first: Zhikun

last: Li

first: Tongtong

last: Cui

first: Guihai

last: Feng

first: Wei

first: Ying

last: Zhang

first: Qi

last: Zhou


title: Transcriptional profiling of parental and immunotherapy-resistant mouse pancreatic tumor cells

first: Jinyang

summary: Pancreatic cancer is largely refractory to immunotherapies. This project utilized mouse pancreatic tumor cell line to study tumor cell intrinsic mechanisms undelrying resistance to immunotherapies. RNA-seq analysis revealed that immunotherapy-resistant tumor cells exhibit increased gene expression signature of epithelial-to-mesenchymal transition, compared to the parental tumor cells.

overall_design: Immunotherapy-resistant tumor cells were derived from a parental mouse pancreatic tumor cell line. This project aims to compare gene expression difference between the parental and derived immunotherapy-resistant tumor cells.

first: Mark

last: Diamond

first: Robert

last: Vonderheide


title: Genome-wide analysis of histone modification alteration in MKN7_EB by EHF knockdown (ChIP-Seq).

first: Masaki

summary: We analysed active enhancers after EBV infection in MKN7_EB and potential EHF motif binding regions by performing ChIP-seq on H3K4me3, H3K4me1 and H3K27ac.

overall_design: Examination of active enhancer binding with EHF motif in MKN7_EB during EBV infection.

first: Wenzhe

first: Atsushi

last: Okabe

last: Kaneda


title: Microglia RNA-seq of mus musculus:adult male dorsal hippocampus

first: Zhilin

address: 138 Yixueyuan Road

summary: Engrams are considered to be substrates for memory storage, and the functional dysregulation of the engrams leads to cognition impairment.However, the cellular basis for these maladaptive changes lead to the forgetting of memories remains unclear. Here we found that the expression of autophagy protein 7 (Atg7) mRNA was dramatically upregulated in aged DG engrams, and led to the forgetting of contextual fear memory and the activation of surrounding microglia.To determine mechanism by which autophagy in DG engrams activates the surrounding microglia, mice were co-injected AAV-RAM-Cre either with AAV-Dio-Atg7-Flag or AAV-Dio- EYFP in dorsal dentate gyrus to overexpress ATG7 in the DG memory engrams. Microglia were separated using magnetic-activated cell sorting and subjected to RNA-Seq in dorsal hippocampus .Bioinformatics analysis shown overexpression of Atg7 in dorsal DG memory engrams caused an increase in the expression of Tlr2  in the surrounding microglia.Depletion of Toll-like receptor 2/4 (TLR2/4) in DG microglia prohibited excessive microglial activation and synapse elimination induced by the overexpression of ATG7 in DG engrams, and thus prevented forgetting. Furthermore, the expression of Rac1, a Rho-GTPases which regulates active forgetting in both fly and mice, was upregulated in aged engrams. Optogentic activation of Rac1 in DG engrams promoted the autophagy of the engrams, the activation of microglia, and the forgetting of fear memory. Invention of the Atg7 expression and microglia activation attenuated forgetting induced by activation of Rac1 in DG engrams. Together, our findings revealed autophagy-dependent synapse elimination of DG engrams by microglia as a novel forgetting mechanism.

overall_design: Mice were co-injected AAV-RAM-Cre either with AAV-Dio-Atg7-Flag or AAV-Dio- EYFP in dorsal dentate gyrus to overexpress ATG7 in the DG memory engrams. Microglia were separated using magnetic-activated cell sorting and subjected to RNA-Seq in dorsal hippocampus .

first: Ruyan

last: Chen

first: Feifei

first: Lan

last: Ma


title: mouse 3T3L1 adipocytes transduced with Lmo3- or LacZ-Adenovirus

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

summary: Background. Obesity and body fat distribution are important risk factors for the development of type 2 diabetes and metabolic syndrome. Evidence has accumulated that this risk is related to intrinsic differences in behavior of adipocytes in different fat depots. LIM Domain Only 3 (LMO3) plays a crucial role in adipogenesis modulating the key adipogenic master switch PPARγ in human, but not mouse, visceral adipose progenitors; however, despite high expression in mature adipocytes, its function in these cells is currently unknown. Aims/Hypothesis. The aim of this study was to determine the potential involvement of LMO3-dependent pathways in the modulation of key functions of mature adipocytes during obesity. Methods. Based on a recently engineered hybrid rAAV serotype Rec2 shown to efficiently transduce both brown adipose tissue (BAT) and white adipose tissue (WAT), we delivered YFP or Lmo3 to epididymal WAT (eWAT) of C57Bl6/J mice on a high fat diet (HFD). The effects of eWAT transduction on metabolic parameters were evaluated 10 weeks later. To further define the role of LMO3 in insulin-stimulated glucose uptake, insulin signaling, adipocyte bioenergetics as well as endocrine function, experiments were conducted in 3T3-L1 adipocytes and newly differentiated human primary mature adipocytes, engineered for transient gain- or loss of LMO3 expression, respectively.Results. AAV transduction of eWAT results in strong and stable Lmo3 expression specifically in the adipocyte fraction over a course of 10 weeks with HFD feeding. Lmo3 expression in eWAT significantly improved glucose clearance and insulin sensitivity in diet-induced obesity, paralleled by increased serum adiponectin. In vitro, Lmo3 expression in 3T3-L1 adipocytes increased insulin-stimulated GLUT4 translocation and glucose uptake as well as mitochondrial oxidative capacity in addition to fatty acid oxidation. On a molecular level, LMO3 augmented PPARg activity, oxidative mitochondrial gene expression, which depended on   and the expression of the PPARg co-activator Ncoa1, which was required for LMO3 effects on mitochondria and glucose uptake. In human mature adipocytes, LMO3 overexpression promoted, while silencing of LMO3 suppressed mitochondrial oxidative capacity. Conclusions. LMO3 expression in visceral adipose tissue regulates multiple genes that preserve adipose tissue functionality during obesity, such as glucose tolerance, insulin sensitivity and adiponectin secretion. Together with increased PPARγ activity, these gene expression changes promote insulin-induced GLUT4 translocation, glucose uptake in addition to increased mitochondrial oxidative capacity, limiting HFD-induced adipose dysfunction. These data add LMO3 as a novel regulator improving visceral adipose tissue function during obesity.

overall_design: De-novo differentiated mature 3T3-L1 adipocytes were transduced with control (LacZ) or Lmo3 overexpressing Adenovirus; RNA was isolated 72 hrs after transduction and subjected to RNA-Seq analysis. RNA was harvested from three separate adenoviral infections per genotype (LacZ and Lmo3, respectively)

first: Martin

last: Bilban

first: Sophia

last: Derdak


title: Transcriptome analysis induced by CTN infection

city: Kunming

first: Jie

last: Song

state: Yunnan

address: Number 935 Jiaoling Load

institute: Institute of Medical Biology, Chinese Academy of Medicine Science and Peking Union Medical College

summary: In this study, we aimed to adopt the transcriptome sequencing technology to obtain the different changes of transcriptome profiles after infecting with CTN in human neuroblastoma cell line SH-SY5Y. And then, through systematic bioinformatics analysis, we hope to find useful clues for the pathogenesis of Rabies.

overall_design: There are 3 samples, including CTN-0h（Control group), CTN-24h and CTN-48h.

first: Shaozhong

last: Dong


title: iPOTs: Internet of Things-based pot system controlling optional treatment of soil water condition for plant phenotyping under drought stress

city: Tsukuba

first: Taiji

last: Kawakatsu

state: Ibaraki

address: 3-1-3 Kan-nondai

institute: National Agriculture and Food Research Organization

summary: A cultivation facility that can assist users in controlling the soil water condition is needed for accurately phenotyping plants under drought stress in an artificial environment. Here we report the Internet of Things (IoT)-based pot system controlling optional treatment of soil water condition (iPOTs), an automatic irrigation system that mimics the drought condition in a growth chamber. The Wi-Fi-enabled iPOTs system allows water supply from the bottom of the pot, based on the soil water level set by the user, and automatically controls the soil water level at a desired depth. The iPOTs also allows users to monitor environmental parameters, such as soil temperature, air temperature, humidity, and light intensity, in each pot. To verify whether the iPOTs mimics the drought condition, we conducted a drought stress test on rice varieties and near-isogenic lines, with diverse root system architecture, using the iPOTs system installed in a growth chamber. Similar to the results of a previous drought stress field trial, the growth of shallow-rooted rice accessions was severely affected by drought stress compared with that of deep-rooted accessions. The microclimate data obtained using the iPOTs system increased the accuracy of plant growth evaluation. Transcriptome analysis revealed that pot positions in the growth chamber had little impact on plant growth. Together, these results suggest that the iPOTs system represents a reliable platform for phenotyping plants under drought stress.

overall_design: RNA-seq from root tips of all crown roots and leaves of two rice accessions, IR64 and Kinandang Patong grown at three different positions in the growth chamber for three weeks.  Plants in this study were not treated with drought stress; all were grown under normal conditions. A,B, or C in sample title indicates position in growth chamber.


title: LMO3 reprogramms viseral adipocyte metabolism during obesity [Mouse]

summary: Aims/Hypothesis. The aim of this study was to determine the potential involvement of LMO3-dependent pathways in the modulation of key functions of mature adipocytes during obesity.   Methods. Based on a recently engineered hybrid rAAV serotype Rec2 shown to efficiently transduce both brown adipose tissue (BAT) and white adipose tissue (WAT), we delivered YFP  or Lmo3 to epididymal WAT (eWAT) of C57Bl6/J mice on a high fat diet (HFD). The effects of eWAT transduction on metabolic parameters were evaluated 10 weeks later. To further define the role of LMO3 in insulin-stimulated glucose uptake, insulin signaling, adipocyte bioenergetics as well as endocrine function, experiments were conducted in 3T3-L1 adipocytes and newly differentiated human primary mature adipocytes, engineered for transient gain- or loss of LMO3 expression, respectively.   Results. AAV transduction of eWAT results in strong and stable Lmo3 expression specifically in the adipocyte fraction over a course of 10 weeks with HFD feeding. Lmo3 expression in eWAT significantly improved glucose clearance and insulin sensitivity in diet-induced obesity, paralleled by increased serum adiponectin. On a molecular level, LMO3 expression in eWAT increased pathways indicative of adipogenesis and PPARg signaling as well as mitochondrial activity, paralleled by a suppression of adipose tissue fibrosis. In vitro, Lmo3 expression in 3T3-L1 adipocytes increased insulin-stimulated GLUT4 translocation and glucose uptake as well as mitochondrial oxidative capacity in addition to fatty acid oxidation. LMO3 overexpression promoted, while silencing of LMO3 suppressed, mitochondrial oxidative capacity in human mature adipocytes.   Conclusions. LMO3 expression in visceral adipose tissue regulates multiple genes that preserve adipose tissue functionality during obesity, such as glucose tolerance, insulin sensitivity and adiponectin secretion. Together with increased PPARγ activity, these gene expression changes promote insulin-induced GLUT4 translocation, glucose uptake in addition to increased mitochondrial oxidative capacity, limiting HFD-induced adipose dysfunction. These data add LMO3 as a novel regulator improving visceral adipose tissue function during obesity.


title: LMO3 reprogramms viseral adipocyte metabolism during obesity

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Expression data from distal colorectal tissues of Pdgfc+/+ and Pdgfc-/- mice with or without irradiation

city: Guangzhou

first: Lekun

last: Fang

address: Yuancunerheng Road

institute: Sun Yat-sen University

summary:
Radiation therapy for malignancies in the pelvic region leads to a crucial complication called radiation proctopathy(RP) with acute changes in bowel habits or long-term morbidity.
We used microarrays to detail the genome-wide profiles of  mice with different genotypes (Pdgfc+/+ and Pdgfc-/- ) under irradiation treatment or not.

overall_design: The distal colorectal tissues of Pdgfc+/+ and Pdgfc-/- mice with or without irradiation were selected for RNA extractionon, amplification, label, hybridization and scan on Affymetrix microarrays, and finally calculated by MAS 5.0 algorithm, Affy packages in R to get the genome-wide profiles of different groups.


title: Examination of CA1 hippocampal DNA methylation as a mechanism for closing of estrogen’s critical window

city: Gainesville

first: Thomas

last: Foster

state: Florida

address: 1149 S. Newell Dr.

department: Neuroscience

institute: University of Florida

type: Methylation profiling by high throughput sequencing

summary: The study presents several novel findings that relate to the idea that alterations in DNA methylation occurs during aging and may be linked to senescent physiology, including a decline in circulating E2. In addition, the evidence has been provided that DNA methylation contributes to the closing of the critical window for E2 effects on synaptic function.

overall_design: The study was conducted on fisher 344 female rats of three different age groups, young (5-6 months, n= 10), middle-age 6-12 months, n= 10) and aged (12-18months, n= 11). Animals were ovariectomized and after 6 weeks injection of estrogen and oil treatmentwere conducted for two consecutive days 24 hours apart. After 6 hours of last injection, CA1 region of brain were collected and stored in -80ᵒC. Genomic DNA was isolated to conduct whole genome bisulfite sequencing to investigate the effect of age and estrogen treatment on the DNA methylome of the CA1 region.

first: Puja

last: Sinha

first: Asha

last: Rani

first: Alberto

last: Riva

first: Ashok

last: Kumar


title: Notum promotes thermogenesis and protects against diet-induced obesity and insulin resistance in mice

city: Los Angeles

first: Alice

last: Mouton

address: 610 Charles E. Young Dr. East

department: Ecology and Evolutionary Biology

institute: UCLA

summary: Notum is a liver-secreted inhibitor of Wnt signaling pathway, which protected against diet induced obesity and improved glucose homeostasis when overexpressed in the mouse liver. Adeno-associated virus (AAV) vectors were used to overexpress green fluorescent protein (GFP) or Notum in the livers of male C57BL/6J mice maintained on a chow diet. Four weeks after the AAV injection, inguinal white adipose tissue (WAT) of these mice were collected to study Notum’s effect on gene expression. RNA-seq analysis of inguinal WAT collected from these mice revealed a highly significant enrichment of extracellular matrix (ECM) gene set among the down-regulated genes in the AAV-Notum group as compared to the AAV-GFP group. These data suggest that Notum inhibits WAT fibrosis, which may be one of the mechanisms by which Notum improves glucose homeostasis.

overall_design: Eight week old male C57BL6/J mice were each injected through the tail vein 1x10^12 genome copies of adeno associated viruses that overexpress either GFP or Notum in a liver specific fashion. After 4 weeks of chow diet feeding, the mice were fasted for 4 hours, euthanized for the collection of inguinal WAT for RNA-seq experiment.

first: Diana

last: Shih


title: Genome-wide analysis of gene expression in MKN7_EB by EHF knockdown (RNA-Seq).

first: Masaki

last: Fukuyo

summary: We analysed gene expression in MKN7_EB regulated by EHF binding enhancer regions, compared with control group.

overall_design: Examination of gene expression in MKN7_EB before and after EHF knockdown.

first: Wenzhe

last: Li

first: Atsushi

last: Okabe

last: Kaneda


title: Genome-wide mapping of QKI-5-RNA interactions in BEAS2B cells by iCLIP-seq

city: Shanghai

first: Xing

last: Fu

address: 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences

summary: iCLIP-seq analysis was performed to identify QKI-5 in vivo binding sites in the human bronchial epithelial BEAS2B cells.

overall_design: iCLIP-seq in BEAS2B cells

first: Feng-Yang

last: Zong

first: Jingyi

last: Hui


title: Comparation of two anti-EphA2 CAR-T constructs

city: Beijing

first: yi

last: hu

address: No.10 Yangfangdian Road

institute: Beijing Shijitan Hospital

summary: We constructed two different third generation anti-EphA2 chimeric antigen receptors(CARs) for glioblastoma treatment. They have the same transmembrane and intracellular domains. The only different is the extracellular domain. T cells transduced with these two different CARs exhibited different anti-tumor capacities and cytokine secretion.  So RNA-seq was used to anaylze the different gene expression archetecture of these two CAR-T cells.

overall_design: Compare two CAR-T cells gene expression profile

first: Zhijing

last: An

first: Yi

last: Hu

first: Xiaosong

last: Zhong


title: Expression data from mandibular condylar cartilage of rats

city: Riyadh

first: Aisha

middle: Mohammed

last: Basudan

state: Riyadh

address: Arrimayah

country: Saudi Arabia

institute: King Abdulaziz Medical City

summary:
Mandibular condylar cartilage (MCC) has many distinctive features reviewed in the literature, hence it would be expected that the genetic regulation of the biological process in the MCC to be different from those of other articular hyaline cartilages and epiphyseal growth cartilages. In addition, The MCC is a multi-zonal fibrocartilage containing different types of cells, which are well characterized histomorphologically, but the factors governing their morphological transition across the zones are not fully understood. Therefore, we can speculate that unique genetic profiles in vivo might exist within the four zones of MCC.
We used microarrays to obtain new insights into the MCC cells by performing a comprehensive zone-specificgene expression profile analysis for each zone of the MCC isolated from 5-week-old rats using LCM technology and compare it to femoral condylar cartilage (FCC) profiles.

overall_design: Sprague-Dawley 5-week-old male rat (Rattus norvegicus) was sacrificed. MCC and FCC specimens were harvested, and then to obtain homogeneous cell populations, we followed our optimized laser-capture microdissection (LCM) protocol described earlier to collect RNA from the four zones of MCC individually thereby four groups: fibrous zone (FZ), proliferative zone (PZ), mature chondrocytes zone (MZ), and hypertrophic chondrocytes zone (HZ) were prepared. Similarly LCM sample was prepared from FCC tissue as a reference sample. LCM-RNA samples were then amplified, labelled, fragmentated, and hybridized  on Affymetrix microarrays chips.

first: Yanq

last: Yan-Qi


title: LMO3 reprogramms viseral adipocyte metabolism during obesity [Human]

first: Markus

last: Jeitler

overall_design: Treated Human mature adipocytes, de-novo differentiated from stromal vascular fraction (SVF) derived from lipoaspirates from 2 different donors. One pool of adipocytes was transfected with a non-targeting siRNA (siCtrl) and the other pool was transfected with a siRNA targeting human LMO3 gene.

first: Martin

last: Bilban


title: Skeletal muscle adaptations to an 8-week weight loss intervention in younger and older obese men

status: Public on Aug 23 2021

city: Toulouse

first: Nathalie

last: Viguerie

address: Avenue Poulhes

country: France

institute: INSERM

summary:
Vastus lateralis Skeletal muscle transcriptomes were analyzed between 13 young  and 12 elderly obese men during a lifestyle intervention.
Lifestyle intervention: Individuals underwent 8-weeks of calorie-restriction of 20% below their daily energy requirement aerobic combined to two sessions of resistance exercise per weeks.

overall_design: Two groups,young and elderly; two conditions for each individual, baseline (before lifestyle intervention) and after  lifestyle intervention.


title: ATP mediates neuropathic pain of neuromyelitis optica spectrum disorder via microglial activation

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Intractable neuropathic pain is recognized as a common symptom of neuromyelitis optica spectrum disorder (NMOSD). However, the underlying mechanism of NMOSD pain remains to be elucidated. Here, we established NMOSD pain model by injecting anti-AQP4 recombinant autoantibodies (AQP4-Ab) generated from NMOSD patient’s plasmablasts into rat spinal cords and confirmed the development of mechanical allodynia. AQP4-Ab mediated extracellular ATP release from astrocytes and pharmacological inhibition of ATP receptor reversed mechanical allodynia in NMOSD pain model. Furthermore, transcriptome analysis revealed microglia activation and IL-1β elevation in NMOSD spinal cord. Inhibition of microglia activation and neutralization of IL-1β also attenuated neuropathic pain in NMOSD rat model. In addition, the human CSF ATP concentration was significantly higher in the acute and remission phase of NMOSD than in multiple sclerosis and other neurological disorder patients. These findings indicate ATP, microglial activation and IL-1β secretion orchestrates the pathogenesis of NMOSD neuropathic pain.

overall_design: RNA-sequencing was performed in spinal cords of either rAQP4 IgG or control IgG treated group.

first: Makoto

last: Kinoshita

last: Motooka


title: A single-cell morpho-transcriptomic map of brassinosteroid action in the Arabidopsis root

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

summary: The effects of brassinosteroid signaling on shoot and root development have been characterized in great detail but did not identify a simple consistent positive or negative impact on a basic cellular parameter. Here we combined digital 3D single-cell shape analysis and single-cell mRNA sequencing to characterize root meristems and mature root segments of brassinosteroid-blind mutants and wildtype. These data demonstrate that brassinosteroid signaling neither affects cell volume nor cell proliferation capacity. Instead, brassinosteroid signaling is essential for the precise orientation of cell division planes and the extent and timing of anisotropic cell expansion. Moreover, we found that the cell-aligning effects of brassinosteroid signaling can propagate to normalize the anatomy of both adjacent and distant brassinosteroid-blind cells through non-cell-autonomous functions, which are sufficient to restore growth vigor. Finally, single-cell transcriptome data discern directly brassinosteroid-responsive genes from genes that can react non-cell-autonomously and highlight arabinogalactans as sentinels of brassinosteroid-dependent anisotropic cell expansion.

overall_design: Single-cell RNA-seq experiments were performed on protoplast cells extracted from the root-tips of 6 day old Arabidopsis thaliana seedlings.

first: Moritz

last: Graeff

first: Surbhi

last: Rana

first: Jos

last: Wendrich

first: Julien

last: Dorier

first: Thomas

last: Eekhout

first: Ana

middle: C

last: Fandino

first: Nicolas

last: Guex

first: George

middle: W

last: Bassel

first: Christian

last: Hardtke


title: CRISPR library knockout screening identified candidate genes whose loss of function confers lapatinib resistance in HER2-amplified GC cells.

city: Farmington

first: Charles

last: Lee

state: Connecticut

address: 10 Discovery Dr

institute: The Jackson Laboratory

summary: To identify genes, whose loss of function confers drug resistance to lapatinib, we performed a genome-wide CRISPR/Cas9 gene knockout screening in two human gastric cancer cell lines harboring HER2 amplification, N87 and OE19, respectively. By performing this study, we identiied a goup of genes associated with lapatinib resistance in HER2-amplified gastric cancer.

overall_design: A pooled GeCKO V2 library were amplified for lentivirus production, and then two biological replicates of N87 and OE19 cells were transduced with the lentivirus containing GeCKO V2 library at a multiplicity of infection (MOI) of 0.3. Puromycin selection was performed before lapatinib treatment on each cell line to enrich successfully transduced cells. After 14 days of lapatinib treatment, the drug-treated and vehicle-treated cells were harvested. Genomic DNA was extracted for PCR amplification and subsequent deep sequencing of the regions containing the sgRNAs.

first: Gang

last: Ning

first: Qihui

last: Zhu


title: Interferon inducible GBPs restrict Burkholderia thailandensis motility induced cell-cell fusion

city: Memphis

first: Geoffrey

last: Neale

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary: Innate immunity responds to pathogens by producing alarm signals and activating pathways that make host cells inhospitable for pathogen replication. The intracellular bacterium Burkholderia thailandensis invades the cytosol, hijacks host actin, and induces cell fusion to spread to adjacent cells, forming multinucleated giant cells (MNGCs) which promotes bacterial replication. We show that type I interferon (IFN) restricts macrophage MNGC formation during B. thailandensis infection. Guanylate-binding proteins (GBPs) expressed downstream of type I IFN were required to restrict MNGC formation through inhibition of Arp2/3-dependent actin motility during infection. GTPase activity and the CAAX prenylation domain were required for GBP2 recruitment to B. thailandensis, which restricted bacterial actin polymerization required for MNGC formation. Consistent with in vitro macrophages, Gbp2-/- Gbp5-/-, GbpChr3-KO mice were more susceptible to intranasal infection with B. thailandensis than wildtype mice. Our findings reveal that IFN and GBPs play a critical role in restricting cell-cell fusion during infection

overall_design: We used microarrays to gene expression profiles in bone marrow-derived macrophages isolated from wild-type and Ifnar1-/- mice after infection with Burkholderia thailandensis

first: David

last: Place

first: Benoit

last: Briard

first: Parimal

last: Samir

first: Thirumala-Devi

last: Kannaganti


title: The role of Aspergillus fumigatus SmiA transcription factor in the miltefosine resistance

city: Ribeirao Preto

first: Gustavo

middle: Henrique

last: Goldman

state: Sao Paulo

address: Avenida do Cafe

country: Brazil

institute: Sao Paulo University

summary: By searching for new drugs against fungal pathogens, we found that miltefosine is active against Aspergillus fumigatus clinical isolates. A library of transcription factors (TF) null mutants was then challenged with this drug and we discovered a novel TF that confers resistance to miltefonise, named here SmiA. By using ChIP-seq, we searched for SmiA targets upon miltefosine treatment.

overall_design: The SmiA-tagged strain was grown for 16 hours at 37oC  in minimum liquid media at 220 rpm and then transferred to RPMI added with 12.5 ug/ml of miltefosine  for 30 minutes (37oC 220 rpm). After crosslinking, the cells were washed and frozen for chromatin extraction and immunoprecipitation.

first: Thaila

last: Fernanda dos Reis

last: Colabardini

first: Fang

last: Wang


title: Genome-wide maps of chromatin H3K36me2  in  Wild Type and Nsd2 Treg cells conditional knock out Treg cells

city: Nanjing

first: Yuchao

last: Jing

state: Jiangsu

address: 101 Longmian Ave Jiangning District

department: Immunology

institute: Nanjing Medical University

summary: Our study aims to characterize the different H3K36me2 modification genes  between Wild Type and Nsd2 Treg cells conditional knock out groups in Treg cells, and find the influenced pathways and functions,  moreover, we can clarify the NSD2 functions in Treg cells. It can be a clue for further Treg cells study.

overall_design: Treg cells H3K36me2 modification genome  profiles of  wild type (WT) and Nsd2 Treg conditional knock out  mice

first: Xiaoming

first: Le

last: Zhang

first: Yuliang


title: Low-temperature prevents side effects of an anti-cancer drug, cyclophosphamide, on organ development: a study of ex vivo organ culture model

city: Sendai

first: Yuta

last: Chiba

state: Miyagi

address: 4-1 Seiryo-cho, Aoba-ku

institute: Tohoku University

summary: Development of chemotherapy has led to a high survival rate of cancer patients; however, severe side effects of anti-cancer drugs, including organ hypoplasia, persists. This study examined the molecular mechanism of the side effects of cyclophosphamide (CPA), a commonly used anti-cancer drug for the treatment of leukemia, and determined how to suppress the side effects using an organ culture system. Treatment with CPA disturbed the growth of tooth germs by inducing apoptosis and suppressing cellular proliferation and differentiation. Furthermore, organs cultured at low-temperature could avoid the CPA-mediated inhibition of organ morphogenesis and differentiation. Cap analysis of gene expression of CPA-treated tooth germ revealed that the expression of genes related to the G1/S cell cycle checkpoint were down-regulated in the CPA-treated tooth germ cultured at low-temperature. In vitro analysis revealed that low-temperature impeded Rb phosphorylation and caused cell cycle arrest at the G1 phase. This can prevent the CPA-mediated cell damage of DNA replication caused by the cross-linking reaction of CPA. Our results revealed that the side effects of CPA on organ development can be avoided by maintaining a low temperature. Further, this study provides a new screening model for assessing the effects of anticancer drugs on organ development.

overall_design: Total RNA was isolated from cultured mouse tooth germ organs E14.5 tooth germs after adding 2.5 mM CPA or DMSO reagent for 3 days at 25°C or 37°C and mRNA profile was generated by Cap Analysis Gene Expression RNA-sequencing, using Illumina Hiseq1500.

first: Tian

last: Tian

first: Kanako

last: Miyazaki

first: Keita

last: Funada

first: Tomomi

last: Yuta

first: Kanji

last: Mizuta

first: Yao

last: Fu

first: Jumpei

last: Kawahara

first: Xue

last: Han

first: Yuna

last: Ando

first: Ami

first: Aya

last: Yamada

first: Tsutomu

last: Iwamoto

first: Seiji

last: Nakamura

first: Ichiro

last: Takahashi

first: Satoshi

last: Fukumoto

first: Keigo

last: Yoshizaki


title: Intergenerational inheritance of trained immunity and heterologous resistance to infections (ATAC-seq)

city: Bonn

first: Branko

last: Cirovic

address: Carl-Troll Str 31

institute: LIMES

summary: Intergenerational inheritance (Inter-I) of phenotypic characteristics has been demonstrated in plants and invertebrates, with epigenetic modifications playing a role in the inheritance of a variety of features such as appearance1, adaptation to stress, or resistance to infections. Here we provide evidence of Inter-I of transcriptional and epigenetic signatures of trained immunity to the progeny of mice that survived a sublethal systemic Candida albicans infection. Intergenerational trained mice (F1) presented with significant cellular, developmental, transcriptional, and epigenetic changes within the bone marrow resident myeloid effector and progenitor cell compartment. These alterations led to an enhanced responsiveness to in vivo endotoxin challenge and Escherichia coli infection, providing the offspring with protection against heterologous infections. These results argue for the contribution of Lamarckian evolutionary processes to protect against infections in vertebrates.

overall_design: Male mice were infected with subletal dose of C. albicans. One month after clearance of the infection, ‘resting’ (mock-infected with PBS, F0R) and the ‘trained’ (C. albicans-infected and recovered, F0T) mice were mated with healthy non-infected females. FACS-enriched granulocyte macrophage progenitors (GMP) from the bone marrow of the offspring (F1T and F1R, respecively) were subjected to chromatin accessability analysis by ATAC-seq.

first: Natalie

last: Katzmarski

first: Jorge

last: Domínguez-Andrés

first: Kristian

last: Händler

first: Joachim

last: Schultze

first: Evangelos

middle: J

last: Giamarellos-Bourboulis

first: Andreas

last: Schlitzer

first: Mihai

last: Netea


title: The Ami and Yami aborigines of Taiwan and their genetic relationship to East Asian and Pacific populations

city: Tartu

first: Tuuli

last: Reisberg

address: Riia 23

country: Estonia

institute: University of Tartu

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: We combined new data with previously published data (PMID: 25877615, 26811443, 29379068, 18292342, 24297229, 27302840, 24395773 and 30846778) to compare phylogenetic relationships of the Ami and Yami aborigenes of Taiwan to groups from mainland Southeast Asia, island Southeast Asia and Oceania.

overall_design: 43 samples were analyzed with the Illumina HumanOmniExpress 24 Genotyping BeadChips and are described herein.

first: Rene

last: Herrera

first: Mait

last: Metspalu

first: Kai

last: Tätte

first: Ene


title: Single cell RNA sequencing of medial and lateral hippocampal network neurons in the mouse

city: Stanford

first: Justus

middle: M

last: Kebschull

state: CA

address: 327 Campus Drive

institute: Stanford University

summary: By comparing single cell transcriptomes of neurons participating in medial vs. lateral hippocampal networks in the mouse, we identify Latrophilin-2 as a molecular marker of the lateral network.

overall_design: We dissected vGlut1Cre+ neurons from P8 mice from 6 subregions: proximal CA1, distal CA1, medial entorhinal cortex, lateral entorhinal cortex, proximal subiculum, and distal subiculum, dissociated the tissue with papain, and performed plate-based SmartSeq2-based single cell RNA sequencing.

first: Daniel

last: Pederick

first: Jan

last: Lui


title: Impaired GSH biosynthesis disrupts eye development and PAX6 function

city: New Haven

first: Brian

last: Thompson

address: 60 College Street

institute: Yale

summary: Glutathione (GSH) is a critical endogenous antioxidant that protects against intracellular oxidative stress.  As such, pathological alterations in GSH levels are linked to a myriad of diseases including cancer, neurodegeneration and cataract.  The rate limiting step in GSH biosynthesis is catalyzed by the glutamate cysteine ligase catalytic subunit (GCLC). The high expression of GCLC in the lens supports the synthesis of millimolar concentrations of GSH in this tissue. Herein, we describe the morphological consequences of deleting (knocking out) Gclc from surface ectoderm-derived ocular tissues (using the Le-Cre transgene; Gclc KO) which includes an overt microphthalmia phenotype and severely disrupted formation of multiple ocular structures (i.e., cornea, iris, lens, retina). Controlling for the Le-Cre transgene revealed that the deletion of Gclc significantly exacerbated the microphthalmia phenotype in Le-Cre hemizygous mice and resulted in dysregulated gene expression that was unique to only the lenses of KO mice. We further characterized the impaired lens development by conducting an RNA-seq experiment on KO and Gclc control (CON) mouse lens at the day of birth. RNA-sequencing revealed significant differences between Gclc knockout (KO) and Gclc control (CON) lenses, including down-regulation of crystallins and lens fiber cell identity genes, and up-regulation of lens epithelial cell identity genes. In addition, genes related to the immune system (e.g., immune system process, inflammatory response, neutrophil chemotaxis) were upregulated, and genes related to eye/lens development were downregulated. TRANSFAC analysis of differentially expressed genes (DEGs) in the lens of Gclc KO mice implicated PAX6 as a key upstream regulator of Gclc KO sensitive genes. This was further supported by a strong positive correlation between the transcriptomes of the lenses of Gclc KO and Pax6 KO mice. Strikingly, the dysregulation of PAX6-regulated genes in Gclc KO mice was observed despite no change in the ocular localization of PAX6 or decrease in the expression of PAX6 in the lens. In vitro experiments demonstrated that suppression of intracellular GSH concentrations resulted in impairment of PAX6 transactivation activity. Taken together, the present results elucidate a novel mechanism wherein intracellular GSH concentrations may modulate PAX6 activity.

overall_design: Examination of gene expression in the lenses of Gclc KO and CON mice aged P1.

first: Vasilis

last: Vasiliou


title: Adipose tissue adaptations to an 8-week weight loss intervention in younger and older obese men,

first: Nathalie

last: Viguerie

summary:
Abdominal subcutaneous adipose tissue transcriptomes were analyzed between 11 young  and 8 elderly obese men during a lifestyle intervention.
Lifestyle intervention: Individuals underwent 8-weeks of calorie-restriction of 20% below their daily energy requirement aerobic combined to two sessions of resistance exercise per weeks.

overall_design: Two groups,young and elderly; two conditions for each individual, baseline (before lifestyle intervention) and after lifestyle intervention.


title: A sensitization-free dimethyl fumarate (DMF) pro-drug, isosorbide di-(methyl fumarate) (IDMF), provides a topical treatment candidate for psoriasis

status: Public on Aug 22 2021

city: Ann Arbor

first: William

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Expression data from mouse heart post transverse aortic constriction (TAC) -surgery 2 weeks

first: Xia

last: Wang

address: No.10 Xitoutiao, You An Men

department: Department of Physiology and Pathophysiology

institute: capital medical university

summary:
A number of mediators that have been found to be involved in the pathogenesis of cardiac hypertrophy affecting gene transcription, protein synthesis, metabolism,autophagy, oxidative stress and inﬂammation. These mediators including nuclear transcription factor, microRNAs and long noncoding RNAs. However, the gene expression profiles signaling pathways in the pressure overload-induced cardiac hypertrophy remain unknown.
All mice were randomly undertaken sham surgery or TAC for 2 weeks. Hearts were harvested 2 weeks following TAC and performed to further analysis.

overall_design: For microarray profiling, the mice heart total RNA was harvested using TRIzol reagent (Invitrogen, Carlsbad, Canada) and purified using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. The amount and quality of RNA were determined using UV-Vis Spectrophotometer (Thermo, NanoDrop 2000, USA) at the absorbance of 260 nm. The mRNA expression profiling was measured using Affymetrix ClariomTM D mouse Array (Affymetrix GeneChip, Santa Clara CA, USA), which contains 65957 gene-level probe sets.

first: Aijuan

last: Qu


title: A sensitization-free dimethyl fumarate (DMF) pro-drug, isosorbide di-(methyl fumarate) (IDMF), provides a topical treatment candidate for psoriasis [microarray]

summary: Dimethyl fumarate (DMF) is an effective oral treatment for psoriasis administered in Europe for nearly 60 years. Its potential, however, has been limited by contact dermatitis that prohibits topical application. This paper characterizes a DMF derivative, isosorbide di-(methyl fumarate) (IDMF), which was designed to have anti-psoriatic effects without skin-sensitizing properties. We show that IDMF exhibits neither genotoxicity nor radiation sensitivity in skin fibroblasts and is non-irritating and non-sensitizing in animal models (rat, rabbit, guinea pig). Microarray analysis of cytokine-stimulated keratinocytes showed that IDMF represses the expression of genes specifically up-regulated in psoriatic skin lesions but not those of other skin diseases. IDMF also down-regulated genes induced by IL-17A and TNF in keratinocytes, as well as predicted targets of NF-κB and the anti-differentiation ncRNA (ANCR). IDMF further stimulated transcription of oxidative stress response genes (NQO1, GPX2, GSR) with stronger Nrf2/ARE activation compared to DMF. Finally, IDMF reduced erythema and scaling while repressing expression of immune response genes in psoriasiform lesions elicited by topical application of imiquimod in mice. These data demonstrate that IDMF exbibits anti-psoriatic activity that is similar or improved compared to DMF, without the harsh skin-sensitizing effects that have prevented topical delivery of the parent molecule.

overall_design: The study evaluated gene expression changes in cytokine-stimulated keratinocytes (IL-17A + IL-22 + TNF) treated with IDMF or water (control, CTL) for 24 hours (n = 2 per treatment).

first: Krzysztof

last: Bojanowski

first: Ratan

middle: K

last: Chaudhuri


title: NMNAT2 Is Downregulated in Glaucomatous RGCs and RGC-Specific Gene Therapy with NMNAT2 Overexpression Rescues Glaucomatous Neurodegeneration and Visual Function

city: Palo Alto

first: Xue

last: Feng

address: 1651 Page Mill road

institute: Stanford

summary: The lack of neuroprotective treatments for retinal ganglion cells (RGCs) and optic nerve (ON) is a central challenge for glaucoma management. Emerging evidence suggests that redox factor NAD+ decline is a hallmark of aging and neurodegenerative diseases including glaucoma. Supplementation with NAD+ precursors and overexpression of the nicotinamide mononucleotide adenylyltransferase (NMNAT), the key enzyme involved in the NAD+ biosynthetic process, have significant neuroprotection effect on glaucoma. Among the three NMNAT isoforms, only NMNAT2 is enriched in neurons, especially in axons, however, its role in glaucoma is not well studied. Here we present the expression levels of the enzymes that involved in NAD+ metabolism in both naïve and glaucomatous mouse RGCs. Intriguingly, NMNAT2 is the dominant form of NMNATs in RGCs and only its mRNA level, but not NMNAT1 or NMNAT3, is significant decreased in glaucomatous RGCs. We then demonstrated proof-of-principal gene therapy strategy of restoring RGC-specific NMNAT2 and NAD+ levels by AAV2-mediated RGC-specific promoter mSncg-driven long half-life NMNAT2 mutant. This gene therapy strategy is further tested in two optic neuropathy models, traumatic ON crush model and ocular hypertension glaucoma model. RGC-specific NMNAT2 overexpression significantly promotes RGC somata and axons survival and preserves visual function in both models. Our studies suggest that the weaking of NMNAT2 expression in glaucomatous RGCs contributes to detrimental NAD+ decline and that modulating RGC intrinsic NMNAT2 level by AAV2-mSncg vector is a potent gene therapy for glaucomatous neuroprotection.

overall_design: RGC mRNA profiles of  naive and SOHU mice

first: Pei

last: Zhuang


title: RNA-seq analysis of Huh7 cells based on NME7 knockdown

city: Changsha

first: Xin

middle: xin

last: Ren

address: Xiangya road 87

institute: Xiangya hospital

summary: Purpose: Analysis of the regulatory network involved in NME7 in liver cancer cells .  Methods: mRNA profiles of Huh7-shNME7 and Huh7-shCtrl group  were generated by deep sequencing,  using Illumina Novaseq platform. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed. Clusterprofiler software was used to perform GO function enrichment analysis and KEGG pathway enrichment analysis of the differential gene sets.  Results: We identified 873 differential genes, of which 420 were up-regulated and 453 were down-regulated. In GO enrichment analysis, the biological process is mainly in purine nucleoside triphosphate metabolic process and oxidative phosphorylation process. KEGG analysis shows that differential genes are enriched in thermogenesis and aminoacyl-tRNA biosynthesis .  Conclusion: Based on RNA-seq analysis, the regulatory network involved in NME7 in liver cancer is depicted.

first: Xinxin

first: Yuezhen

last: Deng

first: Lunquan

last: Sun


title: scRNA-seq of human PCLS

city: Nashville

first: Jonathan

middle: A

last: Kropski

department: Medicine

institute: Vanderbilt University Medical Center

summary: Precision-cut lung slices (PCLS) are increasingly utilized for ex-vivo disease modeling, but a high-resolution characterization of cellular-phenotype stability in PCLS has not been reported. Comparing the single cell transcriptomic profile of human PCLS after five days of culture to freshly isolated human lung tissue, we found striking changes in  endothelial cells and alveolar epithelial cell programs, reflecting both injury and pathways activated in static culture, while  immune cell frequencies and programs remained largely intact and similar to the native lung. These baseline changes should be considered when utilizing PCLS as a model of the human lung.

overall_design: Examination of scRNA-seq of human precision-cut lung slices after 5 days in culture

first: Jennifer

last: Sucre

first: Nichelle

last: Winters

first: Nicholas

middle: E

last: Banovich


title: A sensitization-free dimethyl fumarate (DMF) pro-drug, isosorbide di-(methyl fumarate) (IDMF), provides a topical treatment candidate for psoriasis [RNA-seq]

overall_design: The purpose of this study was to evaluate the effects of IDMF on gene expression in IMQ-treated mouse skin. The study was performed using 4 independent biological replicates (CTL = IMQ-treated skin, n = 1; PLC = placebo/IMQ-treated skin, n = 2; IDMF = IDMF/IMQ-treated skin, n = 1).


title: Transcriptomics changes after IFN-alpha2 treatment following dBRD9-A or DMSO pretreatment in A549 lung epithelial cells

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

summary: These experiments aim at defining first the entirety of Interferon-stimulated gene expression  in A549 in response to treatment with 100 IU/mL IFN-alpha2. The second second aim was to characterize changes to the transcriptome caused by the prior degradation of bromodomain-containing protein9 (BRD9) by the use of a specific BRD9-degrader (dBRD9-A) both in the uninduced and IFN-alpha2-induced conditions.

overall_design: Analysis of 4 groups (e.g. treatment regimens) each containing 3 independent samples. Two groups were pretreated with DMSO following IFN treatment in one of the groups to determine ISG induction in A549 cells. Cells in the remaining two groups were pretreated with the BRD9 degrader dBRD9-A prior to IFN stimulation in one group. Samples from groups that were not treated with IFN following DMSO or dBRD9-A pretreatment serve as controls in this analysis.

first: Jacob

last: Börold

first: Davide

last: Eletto

first: Idoia

last: Busnadiego

first: Nina

last: Mair

first: Eva

last: Moritz

first: Samira

last: Schiefer

first: Nora

last: Schmidt

first: Philipp

last: Petric

first: Wei-Lynn

last: Wong

first: Martin

last: Schwemmle

first: Benjamin

middle: G

last: Hale


title: Bromodomain containing 9 (BRD9) regulates macrophage inflammatory responses and modulates glucocorticoids receptor activity.

city: SCOTTSDALE

first: Zong

last: Wei

state: Arizona

address: 13400 E Shea Blvd

institute: Mayo Clinic


title: Epigenetic reprogramming of sperm in F1 adult male mice with intrauterine hyperglycemia exposure

city: Shanghai

first: Kexin

last: Zou

address: 131 Dongan Rd.

department: School of Medicine

institute: Fudan University

summary: Birth cohort studies and experimental investigations in animals link gestational diabetes mellitus (GDM) with impaired cognitive performance in the first filial generation (F1). We found that intrauterine hyperglycemia exposure resulted in behavior abnormality and cognitional functional disorder of both F1- and F2-GDM male mice. Methylome of sperm of F1 adult male mice from control pregnant mice (F1-C) and GDM pregnant mice (F1-GDM) revealed differentially methylated genes enriched in neurodevelopmental process.

overall_design: Examination of sperm DNA methylation modifications (control pregnant mice (F1-C, n=3) and GDM pregnant mice (F1-GDM, n=3))  . Each sample was obtained from different dams.

first: Guolian

last: Ding


title: Transcriptome profiling of taxane-resistant, castration-resistant prostate cancer cells versus parental control cells

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: The purpose of the study was to assess the transcriptomic differences between taxane-resistant cell lines and parental control cells to identify drivers of resistance.

overall_design: A total of 6 samples were analyzed in this study, C4-2B and DU145 (parental cells), docetaxel-resistant C4-2B and DU145 cell lines TaxR and DTXR, and cabazitaxel-resistant, docetaxel-resistant derivative cell lines, CabR and CTXR. Cell were harvested, RNA was Trizol extracted, and samples submitted for RNA-sequencing.

first: Alan

last: Lombard

first: Allen

last: Gao


title: Transcriptome profiling of castration-resistant prostate cancer cells treated with novel androgen receptor (AR) and AR-V7 inhibitors

summary: The purpose of this study was to characterize the downstream transcriptomic effects of ARVib-mediated degradation of AR/AR-V7, particularly in attenuating AR/AR-V7 target gene expression in prostate cancer cells. Towards this goal, next-generation sequencing (NGS)-based gene expression profiling (RNA-Sequencing; RNA-Seq) was performed on castration-resistant prostate cancer (CRPC) C4-2B MDVR cells that were treated with vehicle control or one of the AR/AR-V7 inhibitors (ARVib), ARVib-7 or ARVib-31.

overall_design: A total of 3 samples were analyzed in this study. The study focused on one castration-resisatnt prostate cancer (CRPC) cell line, LNCaP-C42B-MDVR. Individual cultures of LNCaP-C42B-MDVR were treated with DMSO vehicle control or one of the niclosamide analog AR/AR-V7 inhibitors (ARVibs ), ARVib-7 (analog #7) or ARVib-31 (analog #31). Following treatment of the cells for 24 hours, total RNA was isolated and then submitted for RNA-sequencing analysis.

first: Chengfei

last: Liu


title: Chemicals targeting Lipid binding domain (LBD) of 38γ

status: Public on Aug 21 2021

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary:
We screened 270,000 compounds from an NCI library for the ability to dock with the non-ATP-binding site of p38γ using virtual screen.
The resulting candidate compounds were for cytotoxicity assays to the Hut78 CTCL cell line and identified CSH71 as one of the most promising agents.

overall_design: To show downstream pathway that CSH71-mediated targeting of p38γ, we first isolated RNA and subjected to microarray analysis of treated vs. control cells and observed upregulation of TNF alpha in several top hit  after assesments of its downstream pathways.

first: Xu

middle: H

last: Zhang

first: Steven

middle: T

last: Rosen


title: Hierarchical transcriptional network controls appressorium-mediated plant infection by the rice blast fungus Magnaporthe oryzae

city: Norwich

first: Jitender

last: Cheema

address: Colney lane

country: United Kingdom

institute: JIC

summary: We report that the homeobox trasncription factor called HOX7 controls hyphae-associated genes, autophagy and cell cycle related genes necessary for appressorium development in the rice blast fungus Magnaporthe oryzae. We also report that the ste transcription factor MST12 regulates gene functions involved in septin reorientation.

overall_design: ChIP-seq carried out in liquid mycelium samples at 48h grown in CM of Hox7 fused with 3xFlag

first: Nicholas

last: Talbot

first: Miriam

last: Oses-Ruiz